Palermo signed a total of 10 players in January, with Diego Fabbrini and Alejandro Faurlin the last to arrive on deadline day.
They both made their debuts but ended in a losing cause as second-half goals from Carlos Carmona and German Denis put Atalanta in control before Nelson's late consolation for the hosts.
There was no shortage of effort from Palermo in the early stages. Atalanta goalkeeper Andrea Consigli had to be alert to divert Josip Ilicic's cross-cum-shot away from goal in the second minute and Massimo Donati then skimmed the post with a speculative long-range effort.
Fabbrini got inside the box for a shooting chance in the 19th minute but watched his effort go wide.
At the other end, Carlos Carmona headed Cristiano Del Grosso's header narrowly wide, but Palermo quickly responded with Consigli making a fine save to deny Fabbrini a debut goal.
Stefano Sorrentino had been keeping a watching brief for most of the first half but was called upon in the 37th minute to make a great save that kept out Luigi Giorgi's powerful drive.
And the goalkeeper came to the rescue again in stoppage time when Facundo Parra beat the offside trap to go one-on-one.
Atalanta had found their groove and they did not lose it during the half-time interval.
The second 45 minutes began with Lionel Scaloni's long ball perfectly picking out Giacomo Bonaventura inside the area, only for the striker to blaze over.
However, they had the lead in the 55th minute when Ivan Radovanovic's long-range effort came back off the crossbar and Carmona was on hand to turn in the rebound.
Mauro Boselli, on loan from Wigan, had a pair of chances to bring Palermo level but missed the target both times from good positions inside the area.
And Atalanta took advantage by doubling their lead in the 71st minute when Gugliermo Stendardo found the run of Denis who raced into the area to slot home.
Davide Biondini might have put it to bed with 10 minutes left but blazed over after a fine run.
Instead, Palermo had hope thanks to Nelson's 83rd minute goal, a simple tap-in from Mauro Formica's cross.
They had chances to level, but Boselli fired wide from Formica's cross and in injury time Consigli was on hand to keep out a header from the same player.